GitHub (and Data Science Tools) 🐱 for Psychologists

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# GitHub (and Data Science Tools) <br> 🐱<br> for Psychologists
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.subtitle[
## Wake Forest University
]
.author[
### S. Mason Garrison
]

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<a href="https://DataScience4Psych.github.io/DataScience4Psych/" target="_blank">Data Science for Psychologists</a>
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# Hello world!

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# What is Git? What is GitHub?

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- **Git:** A distributed Version Control System (VCS). 
  - Effectively, it is a tool for easily tracking changes to your code, collaborating, and sharing. 
  - With Git you can track the changes you make to your project so you always have a record of what you’ve worked on and 
  - can easily revert back to an older version if need be. 
  - It also makes working with others easier—groups of people can work together on the same project and merge their changes into one final source!
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<img src="data:image/png;base64,#img/git-logo.png" width="90%" style="display: block; margin: auto;" />
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# What is GitHub?
.pull-left[
- **GitHub:** A web-based platform built that extends Git’s capabilities by providing a web-based interface for collaboration. 
  - It’s widely used for code development, 
  - allowing multiple people to work together on projects. 
  - GitHub hosts your repositories (project folders) and 
  - provides tools for managing changes, reviewing code, and collaborating with others.
]
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<img src="data:image/png;base64,#img/github_logo.png" width="50%" style="display: block; margin: auto;" /><img src="data:image/png;base64,#img/github-mark.png" width="50%" style="display: block; margin: auto;" />
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# Why GitHub for Psychologists?

- **Collaboration Made Easy:** Facilitates seamless collaboration across the globe, essential for multi-center studies and remote teams.
- **Project Management:** Whether it's research data, experimental protocols, or manuscripts, manage all aspects of your projects in one place.
- **Transparency and Reproducibility:** Open-source projects and data sharing align with the principles of open science, enhancing credibility and reproducibility.
- **Educational Tool:** GitHub Classroom enables interactive learning, allowing students to submit assignments and get feedback easily.
- **Streamlined Publishing:** Use platforms like JOSS (The Journal of Open Source Software) to publish tools developed for psychological research, fostering innovation.
- For psychologists, GitHub offers a platform to not only enhance research productivity but also contribute to a more open and collaborative scientific community.

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# Exploring GitHub's Potential for the Psychology Community

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# GitHub for Project Management

- **Centralized Workspace:** Manage your research projects in a single space, accessible to the whole team.
- **Issue Tracking:** Log tasks, bugs, and feature requests as issues to keep track of project progress.
- **Milestones:** Set important project milestones to track progress towards major goals.
- **Project Boards:** Use Kanban-style boards to visualize workflow, from idea to implementation.

.footnote[Learn more about GitHub for project management: [GitHub Project Management](https://docs.github.com/en/issues/trying-out-the-new-projects-experience)]

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## Managing Research Projects and Labs

- **Collaboration at Scale:** GitHub enables team members to work together seamlessly, regardless of their location.
- **Transparency and Reproducibility:** By hosting your lab's projects on GitHub, you ensure that your research processes are transparent and your results are reproducible.
- **Example:** My [R Computing Lab](https://github.com/R-Computing-Lab) demonstrates how labs can manage datasets, code, and collaborate on analysis in real(ish)-time.

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## Teaching Courses

.pull-left[
- **Interactive Learning:** GitHub provides a platform for sharing up-to-date course materials and notes, making learning more interactive and engaging.
- **Version Control for Syllabi:** Easily update and revise syllabi policies, dates etc. (https://smasongarrison.github.io/syllabi/)
- **Examples:** The [Data Science for Psychologists course repository](https://github.com/DataScience4Psych) repository showcases how GitHub can be used to enhance the teaching and learning experience.
]

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### Data Science for Psychologists

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<img src="data:image/png;base64,#img/screenshot_courserepo.png" width="85%" style="display: block; margin: auto;" />
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## Publishing Academic Papers

- **Streamlined Publication Process:** GitHub supports the publishing process with version control and collaboration, making the development and review of manuscripts more efficient.
- **Open Collaboration:** Encourages open and collaborative peer review and feedback from the global community.
- **Example:** The Journal of Open Source Software (JOSS) uses GitHub to manage submissions, reviews, and publication processes.  https://joss.theoj.org/papers/10.21105/joss.06203

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<img src="data:image/png;base64,#img/screenshot_joss_review.png" width="100%" style="display: block; margin: auto;" />
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## Website Hosting with GitHub

- **Showcase Your Work:** GitHub Pages allows researchers and academics to host their professional portfolios, CVs, and even project pages for free.
- **Example:** Visit [S. Mason Garrison's CV](https://smasongarrison.github.io/CV-Tex/SMasonGarrisonCV.pdf) hosted on GitHub for an example of how you can use GitHub Pages to host your academic CV.

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# Intriguing, right?

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# GitHub toolkit overview

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## Terminology Cheat Sheet

- Repositories (Repo)
  - Store your projects in repositories, including all files, revisions, and documentation.

-Branches
  - Work on different versions of a repository at the same time, allowing for parallel development.

- Commits
  - Save changes to your project, creating a transparent history of your work and decisions.

- Pull Requests
  - Propose changes to a project and discuss those changes with project collaborators before merging them.

- Issues
  - Track ideas, enhancements, tasks, or bugs for your projects. Organize with labels, assignees, and milestones.

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# Git and GitHub

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## Version control

- We introduced GitHub as a platform for collaboration
- But it's much more than that...
- It's actually designed for version control

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## Versioning

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## Versioning with human readable messages

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## Why do we need version control?

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# Git and GitHub tips

- Git is a version control system -- like “Track Changes” features from Microsoft Word on steroids. GitHub is the home for your Git-based projects on the internet -- like DropBox but much, much better).

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- There are millions of git commands -- ok, that's an exaggeration, but there are a lot of them -- and very few people know them all. 99% of the time you will use git to add, commit, push, and pull.

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- We will be doing Git things and interfacing with GitHub through RStudio, but if you google for help you might come across methods for doing these things in the command line -- skip that and move on to the next resource unless you feel comfortable trying it out.

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- There is a great resource for working with git and R: [happygitwithr.com](http://happygitwithr.com/). Some of the content in there is beyond the scope of this talk, but it's a good place to look for help.

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## Let's take a tour - Git and GitHub

- Connect an R project to Github repository
- Working with a local and remote repository
- Making a change locally, committing, and pushing
- Making a change on GitHub and pulling

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## Create a GitHub account

.small[
.instructions[
Go to [github.com](https://github.com/), and create an account (unless you already have one). 
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Tips for selecting a username:<sup>✦</sup>

.small[
- Incorporate your actual name.
- Reuse username from other contexts, e.g., Twitter or Slack.
- Pick a username you'll be comfortable revealing to your future boss.
- Shorter is better than longer.
- Be as unique as possible in as few characters as possible.
- Make it timeless. Don't highlight your current university, employer, etc.
- Avoid words laden with special meaning in programming, like `NA`.
]

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.small[ 
<sup>✦</sup> Source: [Happy git with R](http://happygitwithr.com/github-acct.html#username-advice) by Jenny Bryan
]

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## Practical Demonstrations

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# Getting Started with GitHub

1. **Sign Up on GitHub**
   - Visit [GitHub.com](https://github.com/) and create a new account.
   
2. **Create Your First Repository**
   - Click the "+" icon in the top right corner and select "New repository".
   - Name your repository and optionally add a description.

3. **Install Git**
   - Download and install Git from [git-scm.com](https://git-scm.com/).

4. **Configure Git with RStudio**
   - In RStudio, go to Tools > Global Options > Git/SVN and make sure Git is recognized.

5. **Clone a Repository**
   - Use the "New Project" wizard in RStudio to clone your repository for local work.

6. **Resources to Learn More**
   - [GitHub Guides](https://guides.github.com/)
   - [Happy Git and GitHub for the useR](http://happygitwithr.com/)

Start experimenting with small projects to get comfortable with the workflow. Happy coding!

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# Practical Demonstrations: Connecting R to GitHub

## Step 1: Create a New Repository on GitHub

- Go to [GitHub](https://github.com/) and click on "New" in the Repositories tab.
- Name your repository and add a brief description.
- Choose to initialize with a README for an easy start.

## Step 2: Clone the Repository in RStudio

- In RStudio, go to File > New Project > Version Control > Git.
- Paste the URL of your GitHub repository.
- Choose a directory to store the project on your computer.

## Step 3: Make Changes and Commit

- Modify an existing file or create a new file in the RStudio project.
- Go to the Git tab in RStudio, check the files you've changed, and click "Commit".
- Write a commit message describing the changes and commit.

## Step 4: Push Changes to GitHub

- After committing your changes, click the "Push" button in RStudio to update your GitHub repository.
- Your changes are now on GitHub!

## Step 5: Pull Changes from GitHub

- If changes are made on GitHub (by you or collaborators), you can update your local repository by clicking "Pull" in RStudio.

.footnote[For a detailed guide, check out [Happy Git and GitHub for the useR](http://happygitwithr.com/)]

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# Conclusion and Q&A

- Today, we explored how GitHub can revolutionize research and collaboration in psychology.
- We've seen its potential from managing labs to hosting websites.
- Remember, the journey of a thousand miles begins with a single step. Start small and explore!

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## Any Questions?

Feel free to ask any questions now, or reach out to me after the talk via email garrissm@wfu.edu or on github github.com/smasongarrison.